No, a comma is not required here: Only if the framework is intuitive can we proceed with formalizing and exploring its variations. Compare: Only if the framework is intuitive, but not otherwise, can we proceed with formalizing and exploring its variations. (of course, but not otherwise is a redundancy here). I doubt anybody could provide a hard and fast rule—putting commas in the right places is a murky business.
– Michael LoginNov 15 '17 at 18:44

Here's my short and sweet answer: 1. No need for a comma. Otherwise, you would break the flow of your sentence. 2. The order is fine. This is called inversion. It happens when a clause begins with a negative word ("no", "not", "nowhere" et cetera) or phrases like "only" and "rarely". For details, take a look at this post.

Some usage examples:

Nowhere in the regulations does it say that I have to pay an additional fee if my calls are over 10 minutes long.